Starting phenix.real_space_refine on Wed Feb 21 20:22:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4e_25673/02_2024/7t4e_25673.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4e_25673/02_2024/7t4e_25673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4e_25673/02_2024/7t4e_25673.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4e_25673/02_2024/7t4e_25673.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4e_25673/02_2024/7t4e_25673.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4e_25673/02_2024/7t4e_25673.pdb" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12504 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 12216 2.51 5 N 3240 2.21 5 O 3848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "B TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 69": "OD1" <-> "OD2" Residue "H TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19376 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2422 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2422 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2422 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2422 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2422 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2422 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2422 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2422 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 10.06, per 1000 atoms: 0.52 Number of scatterers: 19376 At special positions: 0 Unit cell: (126.225, 126.225, 129.525, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3848 8.00 N 3240 7.00 C 12216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.64 Conformation dependent library (CDL) restraints added in 3.5 seconds 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4528 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 34 sheets defined 6.8% alpha, 71.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.757A pdb=" N GLU B 261 " --> pdb=" O LYS B 258 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 262 " --> pdb=" O GLY B 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 258 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 320 through 324 Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.696A pdb=" N GLU A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 262 " --> pdb=" O GLY A 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 258 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'C' and resid 258 through 262 removed outlier: 3.759A pdb=" N GLU C 261 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 262 " --> pdb=" O GLY C 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 258 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 320 through 324 Processing helix chain 'D' and resid 258 through 262 removed outlier: 3.698A pdb=" N GLU D 261 " --> pdb=" O LYS D 258 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL D 262 " --> pdb=" O GLY D 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 258 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 315 through 319 Processing helix chain 'D' and resid 320 through 324 Processing helix chain 'E' and resid 258 through 262 removed outlier: 3.756A pdb=" N GLU E 261 " --> pdb=" O LYS E 258 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL E 262 " --> pdb=" O GLY E 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 258 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 315 through 319 Processing helix chain 'E' and resid 320 through 324 Processing helix chain 'F' and resid 258 through 262 removed outlier: 3.767A pdb=" N GLU F 261 " --> pdb=" O LYS F 258 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL F 262 " --> pdb=" O GLY F 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 258 through 262' Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 315 through 319 Processing helix chain 'F' and resid 320 through 324 Processing helix chain 'G' and resid 258 through 262 removed outlier: 3.756A pdb=" N GLU G 261 " --> pdb=" O LYS G 258 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL G 262 " --> pdb=" O GLY G 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 258 through 262' Processing helix chain 'G' and resid 263 through 268 Processing helix chain 'G' and resid 315 through 319 Processing helix chain 'G' and resid 320 through 324 Processing helix chain 'H' and resid 258 through 262 removed outlier: 3.820A pdb=" N GLU H 261 " --> pdb=" O LYS H 258 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL H 262 " --> pdb=" O GLY H 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 258 through 262' Processing helix chain 'H' and resid 263 through 268 Processing helix chain 'H' and resid 315 through 319 Processing helix chain 'H' and resid 320 through 324 Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 42 removed outlier: 3.831A pdb=" N GLY B 35 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL B 49 " --> pdb=" O PHE H 40 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE H 40 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY H 35 " --> pdb=" O GLN H 56 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL H 49 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE G 40 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY G 35 " --> pdb=" O GLN G 56 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL G 49 " --> pdb=" O PHE F 40 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE F 40 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY F 35 " --> pdb=" O GLN F 56 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL F 49 " --> pdb=" O PHE E 40 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE E 40 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY E 35 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL E 49 " --> pdb=" O PHE D 40 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE D 40 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY D 35 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL D 49 " --> pdb=" O PHE C 40 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE C 40 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY C 35 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL C 49 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE A 40 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY A 35 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL A 49 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE B 40 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 59 through 68 removed outlier: 4.275A pdb=" N GLY B 92 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY B 275 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA B 152 " --> pdb=" O GLY B 275 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL B 277 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 59 through 68 removed outlier: 4.275A pdb=" N GLY B 92 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 106 through 109 removed outlier: 6.241A pdb=" N SER B 125 " --> pdb=" O TRP B 304 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N TRP B 304 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLY B 127 " --> pdb=" O MET B 302 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N MET B 302 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU B 129 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TYR B 300 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP B 298 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 203 through 210 removed outlier: 6.395A pdb=" N VAL B 216 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS B 210 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LYS B 132 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N SER B 125 " --> pdb=" O TRP B 304 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N TRP B 304 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLY B 127 " --> pdb=" O MET B 302 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N MET B 302 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU B 129 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TYR B 300 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP B 298 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 172 removed outlier: 7.814A pdb=" N GLU B 160 " --> pdb=" O ASP B 199 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ASP B 199 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N GLU H 160 " --> pdb=" O ASP H 199 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASP H 199 " --> pdb=" O GLU H 160 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N GLU G 160 " --> pdb=" O ASP G 199 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ASP G 199 " --> pdb=" O GLU G 160 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLU F 160 " --> pdb=" O ASP F 199 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ASP F 199 " --> pdb=" O GLU F 160 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N GLU E 160 " --> pdb=" O ASP E 199 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ASP E 199 " --> pdb=" O GLU E 160 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLU D 160 " --> pdb=" O ASP D 199 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ASP D 199 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLU C 160 " --> pdb=" O ASP C 199 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ASP C 199 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N GLU A 160 " --> pdb=" O ASP A 199 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ASP A 199 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 59 through 68 removed outlier: 4.188A pdb=" N GLY A 92 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP A 85 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLU A 90 " --> pdb=" O ASP A 85 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY A 275 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA A 152 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL A 277 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 59 through 68 removed outlier: 4.188A pdb=" N GLY A 92 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP A 85 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLU A 90 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 106 through 109 removed outlier: 6.345A pdb=" N SER A 125 " --> pdb=" O TRP A 304 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N TRP A 304 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLY A 127 " --> pdb=" O MET A 302 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET A 302 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU A 129 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TYR A 300 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASP A 298 " --> pdb=" O PRO A 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 203 through 210 removed outlier: 6.387A pdb=" N VAL A 216 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS A 210 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LYS A 132 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N SER A 125 " --> pdb=" O TRP A 304 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N TRP A 304 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLY A 127 " --> pdb=" O MET A 302 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET A 302 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU A 129 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TYR A 300 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASP A 298 " --> pdb=" O PRO A 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 68 removed outlier: 4.256A pdb=" N GLY C 92 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLY C 275 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA C 152 " --> pdb=" O GLY C 275 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL C 277 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 68 removed outlier: 4.256A pdb=" N GLY C 92 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 106 through 109 removed outlier: 6.402A pdb=" N SER C 125 " --> pdb=" O TRP C 304 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N TRP C 304 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLY C 127 " --> pdb=" O MET C 302 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N MET C 302 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU C 129 " --> pdb=" O TYR C 300 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N TYR C 300 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP C 298 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 203 through 210 removed outlier: 6.351A pdb=" N VAL C 216 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS C 210 " --> pdb=" O GLU C 214 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU C 214 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LYS C 132 " --> pdb=" O PHE C 221 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER C 125 " --> pdb=" O TRP C 304 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N TRP C 304 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLY C 127 " --> pdb=" O MET C 302 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N MET C 302 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU C 129 " --> pdb=" O TYR C 300 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N TYR C 300 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP C 298 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 59 through 68 removed outlier: 4.259A pdb=" N GLY D 92 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY D 275 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA D 152 " --> pdb=" O GLY D 275 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL D 277 " --> pdb=" O ILE D 150 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 59 through 68 removed outlier: 4.259A pdb=" N GLY D 92 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 106 through 109 removed outlier: 6.373A pdb=" N SER D 125 " --> pdb=" O TRP D 304 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TRP D 304 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLY D 127 " --> pdb=" O MET D 302 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET D 302 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU D 129 " --> pdb=" O TYR D 300 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TYR D 300 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASP D 298 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 203 through 210 removed outlier: 6.380A pdb=" N VAL D 216 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS D 210 " --> pdb=" O GLU D 214 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU D 214 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LYS D 132 " --> pdb=" O PHE D 221 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER D 125 " --> pdb=" O TRP D 304 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TRP D 304 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLY D 127 " --> pdb=" O MET D 302 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET D 302 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU D 129 " --> pdb=" O TYR D 300 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TYR D 300 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASP D 298 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 59 through 68 removed outlier: 4.256A pdb=" N GLY E 92 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY E 275 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA E 152 " --> pdb=" O GLY E 275 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL E 277 " --> pdb=" O ILE E 150 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 59 through 68 removed outlier: 4.256A pdb=" N GLY E 92 " --> pdb=" O ILE E 83 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 106 through 109 removed outlier: 6.352A pdb=" N SER E 125 " --> pdb=" O TRP E 304 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TRP E 304 " --> pdb=" O SER E 125 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLY E 127 " --> pdb=" O MET E 302 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET E 302 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU E 129 " --> pdb=" O TYR E 300 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TYR E 300 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP E 298 " --> pdb=" O PRO E 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 203 through 210 removed outlier: 6.425A pdb=" N VAL E 216 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS E 210 " --> pdb=" O GLU E 214 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLU E 214 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LYS E 132 " --> pdb=" O PHE E 221 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER E 125 " --> pdb=" O TRP E 304 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TRP E 304 " --> pdb=" O SER E 125 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLY E 127 " --> pdb=" O MET E 302 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET E 302 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU E 129 " --> pdb=" O TYR E 300 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TYR E 300 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP E 298 " --> pdb=" O PRO E 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 59 through 68 removed outlier: 4.279A pdb=" N GLY F 92 " --> pdb=" O ILE F 83 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY F 275 " --> pdb=" O ALA F 152 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA F 152 " --> pdb=" O GLY F 275 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL F 277 " --> pdb=" O ILE F 150 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 59 through 68 removed outlier: 4.279A pdb=" N GLY F 92 " --> pdb=" O ILE F 83 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 106 through 109 removed outlier: 6.251A pdb=" N SER F 125 " --> pdb=" O TRP F 304 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TRP F 304 " --> pdb=" O SER F 125 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLY F 127 " --> pdb=" O MET F 302 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET F 302 " --> pdb=" O GLY F 127 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU F 129 " --> pdb=" O TYR F 300 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR F 300 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASP F 298 " --> pdb=" O PRO F 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 203 through 210 removed outlier: 6.373A pdb=" N VAL F 216 " --> pdb=" O ILE F 208 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS F 210 " --> pdb=" O GLU F 214 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU F 214 " --> pdb=" O LYS F 210 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LYS F 132 " --> pdb=" O PHE F 221 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER F 125 " --> pdb=" O TRP F 304 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TRP F 304 " --> pdb=" O SER F 125 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLY F 127 " --> pdb=" O MET F 302 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET F 302 " --> pdb=" O GLY F 127 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU F 129 " --> pdb=" O TYR F 300 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR F 300 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASP F 298 " --> pdb=" O PRO F 131 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 59 through 68 removed outlier: 4.260A pdb=" N GLY G 92 " --> pdb=" O ILE G 83 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY G 275 " --> pdb=" O ALA G 152 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA G 152 " --> pdb=" O GLY G 275 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL G 277 " --> pdb=" O ILE G 150 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 59 through 68 removed outlier: 4.260A pdb=" N GLY G 92 " --> pdb=" O ILE G 83 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 106 through 109 removed outlier: 6.370A pdb=" N SER G 125 " --> pdb=" O TRP G 304 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TRP G 304 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLY G 127 " --> pdb=" O MET G 302 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N MET G 302 " --> pdb=" O GLY G 127 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU G 129 " --> pdb=" O TYR G 300 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR G 300 " --> pdb=" O LEU G 129 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP G 298 " --> pdb=" O PRO G 131 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 203 through 210 removed outlier: 6.362A pdb=" N VAL G 216 " --> pdb=" O ILE G 208 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS G 210 " --> pdb=" O GLU G 214 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLU G 214 " --> pdb=" O LYS G 210 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LYS G 132 " --> pdb=" O PHE G 221 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N SER G 125 " --> pdb=" O TRP G 304 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TRP G 304 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLY G 127 " --> pdb=" O MET G 302 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N MET G 302 " --> pdb=" O GLY G 127 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU G 129 " --> pdb=" O TYR G 300 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR G 300 " --> pdb=" O LEU G 129 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP G 298 " --> pdb=" O PRO G 131 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 59 through 68 removed outlier: 4.221A pdb=" N GLY H 92 " --> pdb=" O ILE H 83 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY H 275 " --> pdb=" O ALA H 152 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA H 152 " --> pdb=" O GLY H 275 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL H 277 " --> pdb=" O ILE H 150 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 59 through 68 removed outlier: 4.221A pdb=" N GLY H 92 " --> pdb=" O ILE H 83 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 106 through 109 removed outlier: 6.250A pdb=" N SER H 125 " --> pdb=" O TRP H 304 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TRP H 304 " --> pdb=" O SER H 125 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLY H 127 " --> pdb=" O MET H 302 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N MET H 302 " --> pdb=" O GLY H 127 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU H 129 " --> pdb=" O TYR H 300 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TYR H 300 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP H 298 " --> pdb=" O PRO H 131 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 203 through 210 removed outlier: 6.339A pdb=" N VAL H 216 " --> pdb=" O ILE H 208 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS H 210 " --> pdb=" O GLU H 214 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLU H 214 " --> pdb=" O LYS H 210 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LYS H 132 " --> pdb=" O PHE H 221 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N SER H 125 " --> pdb=" O TRP H 304 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TRP H 304 " --> pdb=" O SER H 125 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLY H 127 " --> pdb=" O MET H 302 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N MET H 302 " --> pdb=" O GLY H 127 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU H 129 " --> pdb=" O TYR H 300 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TYR H 300 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP H 298 " --> pdb=" O PRO H 131 " (cutoff:3.500A) 1168 hydrogen bonds defined for protein. 3267 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.83 Time building geometry restraints manager: 7.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6296 1.34 - 1.46: 4114 1.46 - 1.57: 9222 1.57 - 1.69: 0 1.69 - 1.80: 144 Bond restraints: 19776 Sorted by residual: bond pdb=" N SER B 174 " pdb=" CA SER B 174 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.35e+00 bond pdb=" N SER C 174 " pdb=" CA SER C 174 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.27e+00 bond pdb=" CA THR G 70 " pdb=" C THR G 70 " ideal model delta sigma weight residual 1.519 1.529 -0.010 9.50e-03 1.11e+04 1.10e+00 bond pdb=" CG1 ILE E 167 " pdb=" CD1 ILE E 167 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.05e+00 bond pdb=" CG1 ILE D 301 " pdb=" CD1 ILE D 301 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 1.02e+00 ... (remaining 19771 not shown) Histogram of bond angle deviations from ideal: 98.72 - 105.77: 427 105.77 - 112.83: 10544 112.83 - 119.89: 6231 119.89 - 126.95: 9407 126.95 - 134.01: 199 Bond angle restraints: 26808 Sorted by residual: angle pdb=" C TRP H 233 " pdb=" N ASN H 234 " pdb=" CA ASN H 234 " ideal model delta sigma weight residual 121.61 129.71 -8.10 1.39e+00 5.18e-01 3.40e+01 angle pdb=" C TRP A 233 " pdb=" N ASN A 234 " pdb=" CA ASN A 234 " ideal model delta sigma weight residual 121.83 130.76 -8.93 1.56e+00 4.11e-01 3.28e+01 angle pdb=" C SER C 174 " pdb=" CA SER C 174 " pdb=" CB SER C 174 " ideal model delta sigma weight residual 110.42 115.75 -5.33 1.99e+00 2.53e-01 7.18e+00 angle pdb=" C SER B 174 " pdb=" CA SER B 174 " pdb=" CB SER B 174 " ideal model delta sigma weight residual 110.42 115.68 -5.26 1.99e+00 2.53e-01 7.00e+00 angle pdb=" CA TYR E 192 " pdb=" CB TYR E 192 " pdb=" CG TYR E 192 " ideal model delta sigma weight residual 113.90 117.65 -3.75 1.80e+00 3.09e-01 4.33e+00 ... (remaining 26803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 10907 16.94 - 33.87: 788 33.87 - 50.81: 107 50.81 - 67.75: 32 67.75 - 84.69: 38 Dihedral angle restraints: 11872 sinusoidal: 4768 harmonic: 7104 Sorted by residual: dihedral pdb=" CA LYS G 132 " pdb=" C LYS G 132 " pdb=" N LYS G 133 " pdb=" CA LYS G 133 " ideal model delta harmonic sigma weight residual -180.00 -161.16 -18.84 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA LYS C 132 " pdb=" C LYS C 132 " pdb=" N LYS C 133 " pdb=" CA LYS C 133 " ideal model delta harmonic sigma weight residual 180.00 -163.71 -16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA ASN A 140 " pdb=" CB ASN A 140 " pdb=" CG ASN A 140 " pdb=" OD1 ASN A 140 " ideal model delta sinusoidal sigma weight residual 120.00 -172.62 -67.38 2 2.00e+01 2.50e-03 1.02e+01 ... (remaining 11869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1702 0.031 - 0.061: 792 0.061 - 0.092: 195 0.092 - 0.122: 202 0.122 - 0.153: 45 Chirality restraints: 2936 Sorted by residual: chirality pdb=" CA TYR E 192 " pdb=" N TYR E 192 " pdb=" C TYR E 192 " pdb=" CB TYR E 192 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CA ILE H 301 " pdb=" N ILE H 301 " pdb=" C ILE H 301 " pdb=" CB ILE H 301 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA ILE B 301 " pdb=" N ILE B 301 " pdb=" C ILE B 301 " pdb=" CB ILE B 301 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 2933 not shown) Planarity restraints: 3464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 118 " -0.049 5.00e-02 4.00e+02 7.36e-02 8.66e+00 pdb=" N PRO D 119 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN H 118 " 0.048 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO H 119 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO H 119 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO H 119 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 118 " 0.048 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO A 119 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " 0.040 5.00e-02 4.00e+02 ... (remaining 3461 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 312 2.67 - 3.23: 17128 3.23 - 3.79: 29840 3.79 - 4.34: 43004 4.34 - 4.90: 71346 Nonbonded interactions: 161630 Sorted by model distance: nonbonded pdb=" OG SER A 280 " pdb=" OG1 THR A 284 " model vdw 2.117 2.440 nonbonded pdb=" OH TYR G 237 " pdb=" OH TYR G 247 " model vdw 2.177 2.440 nonbonded pdb=" OH TYR C 237 " pdb=" OH TYR C 247 " model vdw 2.177 2.440 nonbonded pdb=" OH TYR D 237 " pdb=" OH TYR D 247 " model vdw 2.188 2.440 nonbonded pdb=" OG SER F 280 " pdb=" OG1 THR F 284 " model vdw 2.199 2.440 ... (remaining 161625 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.020 Extract box with map and model: 4.060 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 50.610 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19776 Z= 0.153 Angle : 0.525 8.932 26808 Z= 0.295 Chirality : 0.046 0.153 2936 Planarity : 0.006 0.074 3464 Dihedral : 12.915 84.687 7344 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2424 helix: -2.80 (0.41), residues: 96 sheet: 0.39 (0.14), residues: 1400 loop : -1.38 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 217 PHE 0.011 0.001 PHE F 100 TYR 0.016 0.001 TYR G 237 ARG 0.005 0.001 ARG H 225 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 829 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 ILE cc_start: 0.7926 (mm) cc_final: 0.7693 (mp) REVERT: B 69 ASP cc_start: 0.6736 (m-30) cc_final: 0.6470 (m-30) REVERT: B 72 ASN cc_start: 0.8115 (m110) cc_final: 0.7829 (m110) REVERT: B 135 ARG cc_start: 0.7618 (tpp80) cc_final: 0.7333 (tpp80) REVERT: B 160 GLU cc_start: 0.7197 (pm20) cc_final: 0.6988 (pm20) REVERT: B 202 ASP cc_start: 0.7115 (m-30) cc_final: 0.6797 (m-30) REVERT: B 231 ASN cc_start: 0.7949 (m110) cc_final: 0.7681 (m-40) REVERT: B 237 TYR cc_start: 0.8205 (m-80) cc_final: 0.7894 (m-80) REVERT: B 294 SER cc_start: 0.8296 (t) cc_final: 0.7866 (m) REVERT: B 308 GLU cc_start: 0.6952 (pm20) cc_final: 0.6579 (pm20) REVERT: A 133 LYS cc_start: 0.8145 (tttm) cc_final: 0.7717 (tttm) REVERT: A 165 ASP cc_start: 0.6765 (m-30) cc_final: 0.6552 (m-30) REVERT: A 226 ASP cc_start: 0.6877 (t0) cc_final: 0.6537 (t0) REVERT: A 237 TYR cc_start: 0.8342 (m-80) cc_final: 0.8113 (m-10) REVERT: A 246 ARG cc_start: 0.7521 (tpp80) cc_final: 0.7165 (tpp80) REVERT: A 258 LYS cc_start: 0.8814 (ptpp) cc_final: 0.8580 (ptpp) REVERT: A 296 MET cc_start: 0.7604 (mpp) cc_final: 0.6962 (mpp) REVERT: A 308 GLU cc_start: 0.7075 (pm20) cc_final: 0.6761 (pm20) REVERT: A 329 GLU cc_start: 0.6535 (mt-10) cc_final: 0.5990 (mt-10) REVERT: C 72 ASN cc_start: 0.7928 (m-40) cc_final: 0.7657 (m110) REVERT: C 202 ASP cc_start: 0.7134 (m-30) cc_final: 0.6844 (m-30) REVERT: C 218 ASP cc_start: 0.6708 (m-30) cc_final: 0.6328 (m-30) REVERT: C 308 GLU cc_start: 0.7002 (pm20) cc_final: 0.6606 (pm20) REVERT: D 36 THR cc_start: 0.8234 (p) cc_final: 0.8025 (m) REVERT: D 112 LYS cc_start: 0.7774 (mttp) cc_final: 0.7530 (mttt) REVERT: D 133 LYS cc_start: 0.8169 (tttm) cc_final: 0.7519 (tttm) REVERT: D 258 LYS cc_start: 0.8734 (ptpp) cc_final: 0.8530 (ptpp) REVERT: D 296 MET cc_start: 0.7155 (mpp) cc_final: 0.6573 (mpp) REVERT: D 308 GLU cc_start: 0.6905 (pm20) cc_final: 0.6541 (pm20) REVERT: E 33 VAL cc_start: 0.8593 (p) cc_final: 0.8254 (t) REVERT: E 61 ILE cc_start: 0.8005 (mm) cc_final: 0.7787 (mp) REVERT: E 69 ASP cc_start: 0.6734 (m-30) cc_final: 0.6440 (m-30) REVERT: E 133 LYS cc_start: 0.8320 (tttm) cc_final: 0.7989 (tttp) REVERT: E 143 ILE cc_start: 0.8504 (mm) cc_final: 0.8259 (mt) REVERT: E 202 ASP cc_start: 0.7023 (m-30) cc_final: 0.6810 (m-30) REVERT: E 308 GLU cc_start: 0.7106 (pm20) cc_final: 0.6785 (pm20) REVERT: F 48 ILE cc_start: 0.8414 (mt) cc_final: 0.8187 (pp) REVERT: F 159 LYS cc_start: 0.7924 (pttm) cc_final: 0.7610 (pttm) REVERT: F 294 SER cc_start: 0.8103 (m) cc_final: 0.7890 (t) REVERT: F 308 GLU cc_start: 0.6834 (pm20) cc_final: 0.6415 (pm20) REVERT: F 329 GLU cc_start: 0.6530 (mt-10) cc_final: 0.6151 (mt-10) REVERT: G 33 VAL cc_start: 0.8559 (p) cc_final: 0.8279 (t) REVERT: G 308 GLU cc_start: 0.7078 (pm20) cc_final: 0.6808 (pm20) REVERT: H 48 ILE cc_start: 0.8433 (mt) cc_final: 0.8219 (pp) REVERT: H 58 ARG cc_start: 0.8753 (ttt180) cc_final: 0.8549 (ttt180) REVERT: H 63 ASN cc_start: 0.7642 (t0) cc_final: 0.7432 (t0) REVERT: H 96 SER cc_start: 0.8347 (m) cc_final: 0.8143 (m) REVERT: H 165 ASP cc_start: 0.6676 (m-30) cc_final: 0.6454 (m-30) REVERT: H 258 LYS cc_start: 0.8688 (ptpp) cc_final: 0.8457 (ptpp) REVERT: H 296 MET cc_start: 0.7475 (mpp) cc_final: 0.7084 (mpp) REVERT: H 308 GLU cc_start: 0.6962 (pm20) cc_final: 0.6562 (pm20) REVERT: H 329 GLU cc_start: 0.6190 (mt-10) cc_final: 0.5971 (mt-10) outliers start: 0 outliers final: 0 residues processed: 829 average time/residue: 1.5312 time to fit residues: 1399.0782 Evaluate side-chains 781 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 781 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 217 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 231 ASN C 316 ASN D 231 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN F 155 ASN F 207 GLN ** G 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 ASN H 140 ASN ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19776 Z= 0.318 Angle : 0.548 8.981 26808 Z= 0.297 Chirality : 0.048 0.166 2936 Planarity : 0.006 0.050 3464 Dihedral : 4.594 17.373 2672 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.90 % Allowed : 12.73 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.17), residues: 2424 helix: -2.60 (0.40), residues: 96 sheet: 0.26 (0.14), residues: 1384 loop : -1.30 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 337 PHE 0.008 0.001 PHE F 100 TYR 0.030 0.001 TYR G 237 ARG 0.007 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 784 time to evaluate : 2.105 Fit side-chains revert: symmetry clash REVERT: B 69 ASP cc_start: 0.6859 (m-30) cc_final: 0.6623 (m-30) REVERT: B 72 ASN cc_start: 0.8192 (m110) cc_final: 0.7749 (m110) REVERT: B 133 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8229 (ttmm) REVERT: B 160 GLU cc_start: 0.7208 (pm20) cc_final: 0.6987 (pm20) REVERT: B 202 ASP cc_start: 0.7137 (m-30) cc_final: 0.6792 (m-30) REVERT: B 237 TYR cc_start: 0.8292 (m-80) cc_final: 0.7997 (m-80) REVERT: B 308 GLU cc_start: 0.7176 (pm20) cc_final: 0.6829 (pm20) REVERT: A 91 MET cc_start: 0.8453 (mtp) cc_final: 0.8211 (mtm) REVERT: A 226 ASP cc_start: 0.7103 (t0) cc_final: 0.6691 (t0) REVERT: A 244 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.6928 (ttp-170) REVERT: A 246 ARG cc_start: 0.7836 (tpp80) cc_final: 0.7273 (tpp80) REVERT: A 296 MET cc_start: 0.7486 (mpp) cc_final: 0.7275 (mpp) REVERT: A 299 MET cc_start: 0.7771 (tpp) cc_final: 0.7451 (mmt) REVERT: A 308 GLU cc_start: 0.7231 (pm20) cc_final: 0.6977 (pm20) REVERT: C 33 VAL cc_start: 0.8494 (p) cc_final: 0.8174 (t) REVERT: C 62 TYR cc_start: 0.8152 (m-80) cc_final: 0.7669 (m-80) REVERT: C 72 ASN cc_start: 0.7901 (m-40) cc_final: 0.7430 (m110) REVERT: C 202 ASP cc_start: 0.7079 (m-30) cc_final: 0.6801 (m-30) REVERT: C 223 GLU cc_start: 0.7303 (pt0) cc_final: 0.7055 (pt0) REVERT: C 246 ARG cc_start: 0.7290 (tpp80) cc_final: 0.7077 (tpp80) REVERT: C 296 MET cc_start: 0.7328 (mpp) cc_final: 0.7072 (mpp) REVERT: C 308 GLU cc_start: 0.7216 (pm20) cc_final: 0.6832 (pm20) REVERT: C 330 ASP cc_start: 0.7433 (p0) cc_final: 0.7230 (p0) REVERT: D 98 ASN cc_start: 0.8061 (m-40) cc_final: 0.7854 (m110) REVERT: D 133 LYS cc_start: 0.8104 (tttm) cc_final: 0.7784 (tttm) REVERT: D 135 ARG cc_start: 0.7915 (tpp80) cc_final: 0.7677 (ttm-80) REVERT: D 159 LYS cc_start: 0.8208 (pttm) cc_final: 0.7907 (pttm) REVERT: D 258 LYS cc_start: 0.8787 (ptpp) cc_final: 0.8547 (ptpp) REVERT: D 308 GLU cc_start: 0.7138 (pm20) cc_final: 0.6815 (pm20) REVERT: E 41 GLU cc_start: 0.7174 (tt0) cc_final: 0.6860 (tt0) REVERT: E 69 ASP cc_start: 0.6791 (m-30) cc_final: 0.6563 (m-30) REVERT: E 133 LYS cc_start: 0.8170 (tttm) cc_final: 0.7683 (tttm) REVERT: E 137 GLU cc_start: 0.6600 (mp0) cc_final: 0.6283 (mp0) REVERT: E 237 TYR cc_start: 0.8242 (m-80) cc_final: 0.7786 (m-10) REVERT: E 258 LYS cc_start: 0.8864 (ptpp) cc_final: 0.8656 (ptpp) REVERT: E 308 GLU cc_start: 0.7279 (pm20) cc_final: 0.6970 (pm20) REVERT: F 69 ASP cc_start: 0.6798 (m-30) cc_final: 0.6516 (m-30) REVERT: F 106 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7072 (ttp80) REVERT: F 132 LYS cc_start: 0.8372 (ttpt) cc_final: 0.8139 (ttpt) REVERT: F 229 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7978 (m) REVERT: F 308 GLU cc_start: 0.7091 (pm20) cc_final: 0.6720 (pm20) REVERT: G 33 VAL cc_start: 0.8515 (p) cc_final: 0.8210 (t) REVERT: G 37 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6668 (mt-10) REVERT: G 70 THR cc_start: 0.8155 (p) cc_final: 0.7915 (p) REVERT: G 106 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7665 (mtp180) REVERT: G 137 GLU cc_start: 0.6873 (mp0) cc_final: 0.6438 (mp0) REVERT: G 208 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8328 (pt) REVERT: G 308 GLU cc_start: 0.7230 (pm20) cc_final: 0.6981 (pm20) REVERT: G 329 GLU cc_start: 0.6596 (mt-10) cc_final: 0.6199 (mt-10) REVERT: H 50 LYS cc_start: 0.8090 (tttp) cc_final: 0.7629 (ttmm) REVERT: H 86 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8445 (mmtp) REVERT: H 98 ASN cc_start: 0.8108 (m-40) cc_final: 0.7891 (m110) REVERT: H 258 LYS cc_start: 0.8771 (ptpp) cc_final: 0.8502 (ptpp) REVERT: H 308 GLU cc_start: 0.7124 (pm20) cc_final: 0.6810 (pm20) outliers start: 41 outliers final: 14 residues processed: 793 average time/residue: 1.6102 time to fit residues: 1400.2290 Evaluate side-chains 779 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 758 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 106 ARG Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 322 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 322 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 148 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 218 optimal weight: 0.7980 chunk 235 optimal weight: 5.9990 chunk 194 optimal weight: 0.3980 chunk 216 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN A 316 ASN C 231 ASN E 282 ASN E 316 ASN F 98 ASN G 282 ASN H 63 ASN ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19776 Z= 0.264 Angle : 0.528 8.217 26808 Z= 0.286 Chirality : 0.047 0.172 2936 Planarity : 0.005 0.059 3464 Dihedral : 4.489 16.330 2672 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.50 % Allowed : 15.93 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.17), residues: 2424 helix: -2.53 (0.41), residues: 96 sheet: 0.21 (0.14), residues: 1384 loop : -1.35 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 217 PHE 0.008 0.001 PHE B 333 TYR 0.025 0.001 TYR G 237 ARG 0.006 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 793 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ASP cc_start: 0.6883 (m-30) cc_final: 0.6646 (m-30) REVERT: B 86 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8344 (mmtp) REVERT: B 108 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8229 (m) REVERT: B 132 LYS cc_start: 0.8350 (ttpp) cc_final: 0.8071 (ttpt) REVERT: B 133 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8070 (ttmm) REVERT: B 160 GLU cc_start: 0.7191 (pm20) cc_final: 0.6936 (pm20) REVERT: B 202 ASP cc_start: 0.7156 (m-30) cc_final: 0.6817 (m-30) REVERT: B 237 TYR cc_start: 0.8421 (m-80) cc_final: 0.8190 (m-10) REVERT: B 308 GLU cc_start: 0.7155 (pm20) cc_final: 0.6795 (pm20) REVERT: A 72 ASN cc_start: 0.7984 (m110) cc_final: 0.7613 (m110) REVERT: A 91 MET cc_start: 0.8401 (mtp) cc_final: 0.8159 (mtm) REVERT: A 133 LYS cc_start: 0.8153 (tttm) cc_final: 0.7923 (tttm) REVERT: A 135 ARG cc_start: 0.8030 (tpp80) cc_final: 0.7600 (tpp80) REVERT: A 226 ASP cc_start: 0.7091 (t0) cc_final: 0.6747 (t70) REVERT: A 244 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.6950 (ttp-170) REVERT: A 246 ARG cc_start: 0.7828 (tpp80) cc_final: 0.7370 (tpp80) REVERT: A 258 LYS cc_start: 0.8823 (ptpt) cc_final: 0.8581 (ptpp) REVERT: A 274 MET cc_start: 0.7534 (mtp) cc_final: 0.7189 (mtp) REVERT: A 296 MET cc_start: 0.7457 (mpp) cc_final: 0.7252 (mpp) REVERT: A 308 GLU cc_start: 0.7220 (pm20) cc_final: 0.6957 (pm20) REVERT: C 33 VAL cc_start: 0.8512 (p) cc_final: 0.8187 (t) REVERT: C 62 TYR cc_start: 0.8164 (m-80) cc_final: 0.7714 (m-80) REVERT: C 202 ASP cc_start: 0.7023 (m-30) cc_final: 0.6780 (m-30) REVERT: C 258 LYS cc_start: 0.8800 (ptpp) cc_final: 0.8590 (ptpp) REVERT: C 308 GLU cc_start: 0.7212 (pm20) cc_final: 0.6829 (pm20) REVERT: C 322 GLU cc_start: 0.7743 (pt0) cc_final: 0.7539 (pt0) REVERT: C 330 ASP cc_start: 0.7428 (p0) cc_final: 0.7223 (p0) REVERT: D 91 MET cc_start: 0.8358 (mtp) cc_final: 0.8069 (mtm) REVERT: D 108 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8255 (m) REVERT: D 132 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7992 (ttpt) REVERT: D 133 LYS cc_start: 0.8029 (tttm) cc_final: 0.7684 (tttm) REVERT: D 135 ARG cc_start: 0.7933 (tpp80) cc_final: 0.7720 (ttm-80) REVERT: D 308 GLU cc_start: 0.7126 (pm20) cc_final: 0.6855 (pm20) REVERT: E 41 GLU cc_start: 0.7174 (tt0) cc_final: 0.6938 (tt0) REVERT: E 69 ASP cc_start: 0.6787 (m-30) cc_final: 0.6565 (m-30) REVERT: E 108 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8227 (m) REVERT: E 133 LYS cc_start: 0.8078 (tttm) cc_final: 0.7788 (tttp) REVERT: E 137 GLU cc_start: 0.6595 (mp0) cc_final: 0.6261 (mp0) REVERT: E 237 TYR cc_start: 0.8257 (m-80) cc_final: 0.7891 (m-10) REVERT: E 258 LYS cc_start: 0.8860 (ptpp) cc_final: 0.8655 (ptpp) REVERT: E 308 GLU cc_start: 0.7272 (pm20) cc_final: 0.6958 (pm20) REVERT: F 69 ASP cc_start: 0.6813 (m-30) cc_final: 0.6534 (m-30) REVERT: F 90 GLU cc_start: 0.6968 (pm20) cc_final: 0.6739 (pm20) REVERT: F 106 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7038 (ttp80) REVERT: F 132 LYS cc_start: 0.8418 (ttpt) cc_final: 0.8211 (ttpt) REVERT: F 229 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7976 (m) REVERT: F 308 GLU cc_start: 0.7110 (pm20) cc_final: 0.6790 (pm20) REVERT: G 33 VAL cc_start: 0.8549 (p) cc_final: 0.8233 (t) REVERT: G 37 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6630 (mt-10) REVERT: G 70 THR cc_start: 0.8138 (p) cc_final: 0.7931 (p) REVERT: G 106 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7634 (mtp180) REVERT: G 137 GLU cc_start: 0.6891 (mp0) cc_final: 0.6456 (mp0) REVERT: G 208 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8330 (pt) REVERT: G 296 MET cc_start: 0.7214 (mpp) cc_final: 0.6936 (mpp) REVERT: G 308 GLU cc_start: 0.7193 (pm20) cc_final: 0.6933 (pm20) REVERT: G 329 GLU cc_start: 0.6476 (mt-10) cc_final: 0.6214 (mt-10) REVERT: H 50 LYS cc_start: 0.8099 (tttp) cc_final: 0.7588 (tttm) REVERT: H 98 ASN cc_start: 0.8112 (m-40) cc_final: 0.7912 (m110) REVERT: H 151 THR cc_start: 0.7967 (p) cc_final: 0.7750 (m) REVERT: H 159 LYS cc_start: 0.8137 (pttm) cc_final: 0.7500 (pttm) REVERT: H 308 GLU cc_start: 0.7134 (pm20) cc_final: 0.6818 (pm20) outliers start: 54 outliers final: 21 residues processed: 806 average time/residue: 1.6119 time to fit residues: 1426.1490 Evaluate side-chains 803 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 771 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 106 ARG Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 169 TYR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 298 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 219 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 114 optimal weight: 0.0770 chunk 207 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN B 316 ASN C 72 ASN C 231 ASN H 63 ASN H 155 ASN H 207 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19776 Z= 0.260 Angle : 0.526 7.749 26808 Z= 0.284 Chirality : 0.047 0.162 2936 Planarity : 0.005 0.064 3464 Dihedral : 4.470 16.511 2672 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.82 % Allowed : 17.45 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.17), residues: 2424 helix: -2.44 (0.42), residues: 96 sheet: 0.25 (0.14), residues: 1400 loop : -1.50 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 217 PHE 0.008 0.001 PHE B 333 TYR 0.023 0.001 TYR G 237 ARG 0.006 0.001 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 805 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 TYR cc_start: 0.8335 (m-80) cc_final: 0.7417 (m-80) REVERT: B 69 ASP cc_start: 0.6840 (m-30) cc_final: 0.6612 (m-30) REVERT: B 108 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8212 (t) REVERT: B 133 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8042 (ttmm) REVERT: B 160 GLU cc_start: 0.7177 (pm20) cc_final: 0.6901 (pm20) REVERT: B 202 ASP cc_start: 0.7169 (m-30) cc_final: 0.6834 (m-30) REVERT: B 237 TYR cc_start: 0.8398 (m-80) cc_final: 0.8193 (m-10) REVERT: B 308 GLU cc_start: 0.7167 (pm20) cc_final: 0.6877 (pm20) REVERT: A 91 MET cc_start: 0.8393 (mtp) cc_final: 0.8146 (mtm) REVERT: A 133 LYS cc_start: 0.8132 (tttm) cc_final: 0.7909 (tttm) REVERT: A 135 ARG cc_start: 0.8032 (tpp80) cc_final: 0.7603 (tpp80) REVERT: A 226 ASP cc_start: 0.7142 (t0) cc_final: 0.6748 (t0) REVERT: A 246 ARG cc_start: 0.7779 (tpp80) cc_final: 0.7206 (mpp80) REVERT: A 258 LYS cc_start: 0.8822 (ptpt) cc_final: 0.8602 (ptpp) REVERT: A 296 MET cc_start: 0.7453 (mpp) cc_final: 0.7231 (mpp) REVERT: A 308 GLU cc_start: 0.7226 (pm20) cc_final: 0.6994 (pm20) REVERT: C 33 VAL cc_start: 0.8516 (p) cc_final: 0.8182 (t) REVERT: C 62 TYR cc_start: 0.8152 (m-80) cc_final: 0.7766 (m-80) REVERT: C 72 ASN cc_start: 0.7964 (m-40) cc_final: 0.7382 (m110) REVERT: C 108 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8237 (t) REVERT: C 202 ASP cc_start: 0.7047 (m-30) cc_final: 0.6813 (m-30) REVERT: C 258 LYS cc_start: 0.8753 (ptpp) cc_final: 0.8533 (ptpp) REVERT: C 302 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7797 (tpp) REVERT: C 308 GLU cc_start: 0.7233 (pm20) cc_final: 0.6850 (pm20) REVERT: C 322 GLU cc_start: 0.7738 (pt0) cc_final: 0.7534 (pt0) REVERT: C 330 ASP cc_start: 0.7410 (p0) cc_final: 0.7209 (p0) REVERT: D 91 MET cc_start: 0.8346 (mtp) cc_final: 0.8037 (mtm) REVERT: D 108 VAL cc_start: 0.8466 (OUTLIER) cc_final: 0.8263 (m) REVERT: D 112 LYS cc_start: 0.7766 (mttp) cc_final: 0.7473 (mttm) REVERT: D 132 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8057 (ttpt) REVERT: D 133 LYS cc_start: 0.8070 (tttm) cc_final: 0.7694 (tttm) REVERT: D 135 ARG cc_start: 0.7917 (tpp80) cc_final: 0.7712 (ttm-80) REVERT: D 308 GLU cc_start: 0.7109 (pm20) cc_final: 0.6833 (pm20) REVERT: D 329 GLU cc_start: 0.6735 (mt-10) cc_final: 0.6458 (mt-10) REVERT: E 37 GLU cc_start: 0.7085 (tt0) cc_final: 0.6825 (tt0) REVERT: E 41 GLU cc_start: 0.7163 (tt0) cc_final: 0.6935 (tt0) REVERT: E 69 ASP cc_start: 0.6787 (m-30) cc_final: 0.6577 (m-30) REVERT: E 108 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8240 (t) REVERT: E 133 LYS cc_start: 0.8053 (tttm) cc_final: 0.7579 (tttp) REVERT: E 137 GLU cc_start: 0.6597 (mp0) cc_final: 0.6280 (mp0) REVERT: E 237 TYR cc_start: 0.8250 (m-80) cc_final: 0.7991 (m-80) REVERT: E 258 LYS cc_start: 0.8845 (ptpp) cc_final: 0.8605 (ptpp) REVERT: E 296 MET cc_start: 0.7413 (mpp) cc_final: 0.6871 (mpp) REVERT: E 308 GLU cc_start: 0.7294 (pm20) cc_final: 0.6982 (pm20) REVERT: F 69 ASP cc_start: 0.6817 (m-30) cc_final: 0.6544 (m-30) REVERT: F 90 GLU cc_start: 0.6951 (pm20) cc_final: 0.6714 (pm20) REVERT: F 229 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7979 (m) REVERT: F 244 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7307 (ttp-170) REVERT: F 246 ARG cc_start: 0.7717 (tpp80) cc_final: 0.7382 (tpp80) REVERT: F 308 GLU cc_start: 0.7109 (pm20) cc_final: 0.6801 (pm20) REVERT: G 33 VAL cc_start: 0.8551 (p) cc_final: 0.8233 (t) REVERT: G 37 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6623 (mt-10) REVERT: G 70 THR cc_start: 0.8126 (p) cc_final: 0.7913 (p) REVERT: G 106 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7628 (mtp180) REVERT: G 137 GLU cc_start: 0.6878 (mp0) cc_final: 0.6488 (mp0) REVERT: G 208 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8317 (pt) REVERT: G 308 GLU cc_start: 0.7133 (pm20) cc_final: 0.6855 (pm20) REVERT: G 329 GLU cc_start: 0.6507 (mt-10) cc_final: 0.6232 (mt-10) REVERT: H 50 LYS cc_start: 0.8083 (tttp) cc_final: 0.7306 (tttm) REVERT: H 63 ASN cc_start: 0.7796 (t0) cc_final: 0.7530 (t0) REVERT: H 98 ASN cc_start: 0.8123 (m-40) cc_final: 0.7920 (m110) REVERT: H 135 ARG cc_start: 0.8064 (tpp80) cc_final: 0.7623 (ttp-170) REVERT: H 159 LYS cc_start: 0.8126 (pttm) cc_final: 0.7483 (pttm) REVERT: H 308 GLU cc_start: 0.7181 (pm20) cc_final: 0.6873 (pm20) REVERT: H 329 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6225 (mt-10) outliers start: 61 outliers final: 27 residues processed: 816 average time/residue: 1.6393 time to fit residues: 1465.1331 Evaluate side-chains 825 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 786 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 327 MET Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 244 ARG Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 329 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN A 239 ASN D 72 ASN D 239 ASN H 72 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 19776 Z= 0.402 Angle : 0.574 8.307 26808 Z= 0.310 Chirality : 0.049 0.172 2936 Planarity : 0.005 0.061 3464 Dihedral : 4.735 20.728 2672 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.19 % Allowed : 18.15 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.17), residues: 2424 helix: -3.93 (0.26), residues: 48 sheet: 0.26 (0.14), residues: 1360 loop : -1.15 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 337 PHE 0.011 0.001 PHE B 333 TYR 0.030 0.001 TYR G 237 ARG 0.007 0.001 ARG E 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 796 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 TYR cc_start: 0.8373 (m-80) cc_final: 0.7587 (m-80) REVERT: B 69 ASP cc_start: 0.6876 (m-30) cc_final: 0.6660 (m-30) REVERT: B 133 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8069 (ttmm) REVERT: B 160 GLU cc_start: 0.7154 (pm20) cc_final: 0.6831 (pm20) REVERT: B 202 ASP cc_start: 0.7188 (m-30) cc_final: 0.6865 (m-30) REVERT: B 308 GLU cc_start: 0.7235 (pm20) cc_final: 0.6963 (pm20) REVERT: A 91 MET cc_start: 0.8433 (mtp) cc_final: 0.8188 (mtm) REVERT: A 226 ASP cc_start: 0.7233 (t0) cc_final: 0.6813 (t0) REVERT: A 308 GLU cc_start: 0.7304 (pm20) cc_final: 0.7100 (pm20) REVERT: C 202 ASP cc_start: 0.7064 (m-30) cc_final: 0.6863 (m-30) REVERT: C 258 LYS cc_start: 0.8748 (ptpp) cc_final: 0.8520 (ptpp) REVERT: C 302 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7828 (tpp) REVERT: C 308 GLU cc_start: 0.7312 (pm20) cc_final: 0.6948 (pm20) REVERT: C 322 GLU cc_start: 0.7746 (pt0) cc_final: 0.7542 (pt0) REVERT: C 330 ASP cc_start: 0.7438 (p0) cc_final: 0.7211 (p0) REVERT: D 132 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8025 (ttpt) REVERT: D 133 LYS cc_start: 0.8100 (tttm) cc_final: 0.7757 (tttm) REVERT: D 308 GLU cc_start: 0.7219 (pm20) cc_final: 0.6959 (pm20) REVERT: D 321 LYS cc_start: 0.7875 (mtpp) cc_final: 0.7662 (mtpp) REVERT: D 329 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6489 (mt-10) REVERT: E 37 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6874 (tt0) REVERT: E 41 GLU cc_start: 0.7172 (tt0) cc_final: 0.6952 (tt0) REVERT: E 133 LYS cc_start: 0.8026 (tttm) cc_final: 0.7741 (tttm) REVERT: E 137 GLU cc_start: 0.6616 (mp0) cc_final: 0.6320 (mp0) REVERT: E 228 TYR cc_start: 0.8528 (m-80) cc_final: 0.8324 (m-80) REVERT: E 237 TYR cc_start: 0.8313 (m-80) cc_final: 0.8038 (m-80) REVERT: E 258 LYS cc_start: 0.8839 (ptpp) cc_final: 0.8600 (ptpp) REVERT: E 274 MET cc_start: 0.7657 (mtp) cc_final: 0.7278 (mtp) REVERT: E 302 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7700 (tpp) REVERT: E 308 GLU cc_start: 0.7354 (pm20) cc_final: 0.7054 (pm20) REVERT: E 329 GLU cc_start: 0.6614 (mt-10) cc_final: 0.6405 (mt-10) REVERT: F 69 ASP cc_start: 0.6837 (m-30) cc_final: 0.6562 (m-30) REVERT: F 90 GLU cc_start: 0.6979 (pm20) cc_final: 0.6725 (pm20) REVERT: F 91 MET cc_start: 0.8304 (mtm) cc_final: 0.8095 (mtp) REVERT: F 229 THR cc_start: 0.8193 (OUTLIER) cc_final: 0.7992 (m) REVERT: F 244 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7367 (ttp-170) REVERT: F 246 ARG cc_start: 0.7833 (tpp80) cc_final: 0.7175 (mpp80) REVERT: F 308 GLU cc_start: 0.7227 (pm20) cc_final: 0.6938 (pm20) REVERT: G 37 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6632 (mt-10) REVERT: G 70 THR cc_start: 0.8189 (p) cc_final: 0.7984 (p) REVERT: G 133 LYS cc_start: 0.8467 (tttm) cc_final: 0.8063 (tttp) REVERT: G 137 GLU cc_start: 0.6868 (mp0) cc_final: 0.6453 (mp0) REVERT: G 296 MET cc_start: 0.7358 (mpp) cc_final: 0.6950 (mpp) REVERT: G 299 MET cc_start: 0.8022 (tpp) cc_final: 0.7711 (mmt) REVERT: G 308 GLU cc_start: 0.7180 (pm20) cc_final: 0.6868 (pm20) REVERT: G 329 GLU cc_start: 0.6632 (mt-10) cc_final: 0.6290 (mt-10) REVERT: H 50 LYS cc_start: 0.8162 (tttp) cc_final: 0.7690 (tttm) REVERT: H 98 ASN cc_start: 0.8152 (m-40) cc_final: 0.7936 (m110) REVERT: H 135 ARG cc_start: 0.8165 (tpp80) cc_final: 0.7807 (ttp-170) REVERT: H 159 LYS cc_start: 0.8131 (pttm) cc_final: 0.7531 (pttm) REVERT: H 231 ASN cc_start: 0.8167 (m110) cc_final: 0.7916 (m110) REVERT: H 308 GLU cc_start: 0.7276 (pm20) cc_final: 0.7043 (pm20) REVERT: H 329 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6293 (mt-10) outliers start: 69 outliers final: 32 residues processed: 809 average time/residue: 1.7039 time to fit residues: 1515.8441 Evaluate side-chains 836 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 795 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 GLU Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 244 ARG Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain G residue 340 ARG Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 329 GLU Chi-restraints excluded: chain H residue 338 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 232 optimal weight: 0.0370 chunk 192 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN C 72 ASN C 231 ASN D 72 ASN D 98 ASN E 231 ASN F 316 ASN H 63 ASN H 72 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19776 Z= 0.313 Angle : 0.553 8.016 26808 Z= 0.299 Chirality : 0.048 0.174 2936 Planarity : 0.005 0.064 3464 Dihedral : 4.647 19.880 2672 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.92 % Allowed : 20.00 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.17), residues: 2424 helix: -3.90 (0.27), residues: 48 sheet: 0.22 (0.14), residues: 1360 loop : -1.12 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 337 PHE 0.009 0.001 PHE B 333 TYR 0.028 0.001 TYR G 237 ARG 0.008 0.001 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 785 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ASP cc_start: 0.6870 (m-30) cc_final: 0.6653 (m-30) REVERT: B 160 GLU cc_start: 0.7134 (pm20) cc_final: 0.6827 (pm20) REVERT: B 167 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7974 (tp) REVERT: B 202 ASP cc_start: 0.7141 (m-30) cc_final: 0.6858 (m-30) REVERT: B 303 ARG cc_start: 0.8309 (mtt90) cc_final: 0.8062 (mtt180) REVERT: B 308 GLU cc_start: 0.7190 (pm20) cc_final: 0.6910 (pm20) REVERT: A 91 MET cc_start: 0.8389 (mtp) cc_final: 0.8137 (mtm) REVERT: A 226 ASP cc_start: 0.7226 (t0) cc_final: 0.6799 (t0) REVERT: A 308 GLU cc_start: 0.7279 (pm20) cc_final: 0.7077 (pm20) REVERT: C 258 LYS cc_start: 0.8712 (ptpp) cc_final: 0.8505 (ptpp) REVERT: C 308 GLU cc_start: 0.7309 (pm20) cc_final: 0.6926 (pm20) REVERT: C 322 GLU cc_start: 0.7739 (pt0) cc_final: 0.7526 (pt0) REVERT: C 330 ASP cc_start: 0.7438 (p0) cc_final: 0.7211 (p0) REVERT: D 308 GLU cc_start: 0.7175 (pm20) cc_final: 0.6916 (pm20) REVERT: D 321 LYS cc_start: 0.7869 (mtpp) cc_final: 0.7651 (mtpp) REVERT: D 329 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6459 (mt-10) REVERT: E 37 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6871 (tt0) REVERT: E 41 GLU cc_start: 0.7164 (tt0) cc_final: 0.6935 (tt0) REVERT: E 62 TYR cc_start: 0.8238 (m-80) cc_final: 0.7414 (m-80) REVERT: E 133 LYS cc_start: 0.8033 (tttm) cc_final: 0.7745 (tttp) REVERT: E 137 GLU cc_start: 0.6632 (mp0) cc_final: 0.6341 (mp0) REVERT: E 237 TYR cc_start: 0.8292 (m-80) cc_final: 0.8076 (m-10) REVERT: E 274 MET cc_start: 0.7600 (mtp) cc_final: 0.7215 (mtp) REVERT: E 302 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7692 (tpp) REVERT: E 308 GLU cc_start: 0.7334 (pm20) cc_final: 0.7029 (pm20) REVERT: E 329 GLU cc_start: 0.6664 (mt-10) cc_final: 0.6358 (mt-10) REVERT: E 330 ASP cc_start: 0.7366 (p0) cc_final: 0.7160 (p0) REVERT: F 69 ASP cc_start: 0.6830 (m-30) cc_final: 0.6557 (m-30) REVERT: F 90 GLU cc_start: 0.7012 (pm20) cc_final: 0.6755 (pm20) REVERT: F 229 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.8009 (m) REVERT: F 246 ARG cc_start: 0.7826 (tpp80) cc_final: 0.7243 (mpp80) REVERT: F 308 GLU cc_start: 0.7194 (pm20) cc_final: 0.6939 (pm20) REVERT: G 33 VAL cc_start: 0.8510 (p) cc_final: 0.8178 (t) REVERT: G 37 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6626 (mt-10) REVERT: G 70 THR cc_start: 0.8167 (p) cc_final: 0.7943 (p) REVERT: G 135 ARG cc_start: 0.8165 (tpp80) cc_final: 0.7881 (tpp80) REVERT: G 137 GLU cc_start: 0.6869 (mp0) cc_final: 0.6471 (mp0) REVERT: G 308 GLU cc_start: 0.7135 (pm20) cc_final: 0.6820 (pm20) REVERT: G 329 GLU cc_start: 0.6650 (mt-10) cc_final: 0.6323 (mt-10) REVERT: H 50 LYS cc_start: 0.8120 (tttp) cc_final: 0.7634 (tttm) REVERT: H 135 ARG cc_start: 0.8168 (tpp80) cc_final: 0.7807 (ttp-170) REVERT: H 159 LYS cc_start: 0.8148 (pttm) cc_final: 0.7570 (pttm) REVERT: H 231 ASN cc_start: 0.8122 (m110) cc_final: 0.7900 (m110) REVERT: H 308 GLU cc_start: 0.7261 (pm20) cc_final: 0.7019 (pm20) REVERT: H 329 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.6139 (mt-10) outliers start: 63 outliers final: 44 residues processed: 799 average time/residue: 1.6961 time to fit residues: 1482.3549 Evaluate side-chains 817 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 767 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 GLU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 128 MET Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 274 MET Chi-restraints excluded: chain H residue 298 ASP Chi-restraints excluded: chain H residue 329 GLU Chi-restraints excluded: chain H residue 338 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 195 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN A 239 ASN C 72 ASN C 231 ASN E 231 ASN H 63 ASN H 72 ASN H 98 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19776 Z= 0.222 Angle : 0.537 7.939 26808 Z= 0.290 Chirality : 0.047 0.157 2936 Planarity : 0.005 0.064 3464 Dihedral : 4.488 19.998 2672 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.73 % Allowed : 20.42 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.17), residues: 2424 helix: -2.32 (0.42), residues: 96 sheet: 0.15 (0.14), residues: 1400 loop : -1.49 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 217 PHE 0.009 0.001 PHE F 100 TYR 0.024 0.001 TYR G 237 ARG 0.008 0.001 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 791 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ASP cc_start: 0.6833 (m-30) cc_final: 0.6619 (m-30) REVERT: B 202 ASP cc_start: 0.7156 (m-30) cc_final: 0.6888 (m-30) REVERT: B 308 GLU cc_start: 0.7164 (pm20) cc_final: 0.6871 (pm20) REVERT: A 226 ASP cc_start: 0.7182 (t0) cc_final: 0.6735 (t0) REVERT: A 308 GLU cc_start: 0.7248 (pm20) cc_final: 0.7039 (pm20) REVERT: C 33 VAL cc_start: 0.8515 (p) cc_final: 0.8175 (t) REVERT: C 258 LYS cc_start: 0.8698 (ptpp) cc_final: 0.8496 (ptpp) REVERT: C 308 GLU cc_start: 0.7310 (pm20) cc_final: 0.6989 (pm20) REVERT: C 322 GLU cc_start: 0.7733 (pt0) cc_final: 0.7521 (pt0) REVERT: C 330 ASP cc_start: 0.7405 (p0) cc_final: 0.7193 (p0) REVERT: D 72 ASN cc_start: 0.8275 (m110) cc_final: 0.8006 (m110) REVERT: D 91 MET cc_start: 0.8347 (mtp) cc_final: 0.8070 (mtm) REVERT: D 308 GLU cc_start: 0.7117 (pm20) cc_final: 0.6834 (pm20) REVERT: D 321 LYS cc_start: 0.7841 (mtpp) cc_final: 0.7623 (mtpp) REVERT: D 329 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6416 (mt-10) REVERT: E 37 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6835 (tt0) REVERT: E 41 GLU cc_start: 0.7153 (tt0) cc_final: 0.6928 (tt0) REVERT: E 72 ASN cc_start: 0.8073 (m110) cc_final: 0.7713 (m110) REVERT: E 137 GLU cc_start: 0.6613 (mp0) cc_final: 0.6326 (mp0) REVERT: E 274 MET cc_start: 0.7511 (mtp) cc_final: 0.7156 (mtp) REVERT: E 286 LYS cc_start: 0.8269 (mttt) cc_final: 0.8065 (mttp) REVERT: E 296 MET cc_start: 0.7417 (mpp) cc_final: 0.6848 (mpp) REVERT: E 302 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7695 (tpp) REVERT: E 308 GLU cc_start: 0.7318 (pm20) cc_final: 0.7021 (pm20) REVERT: E 329 GLU cc_start: 0.6694 (mt-10) cc_final: 0.6320 (mt-10) REVERT: F 69 ASP cc_start: 0.6799 (m-30) cc_final: 0.6532 (m-30) REVERT: F 90 GLU cc_start: 0.6975 (pm20) cc_final: 0.6753 (pm20) REVERT: F 132 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7967 (ttmt) REVERT: F 229 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7999 (m) REVERT: F 246 ARG cc_start: 0.7796 (tpp80) cc_final: 0.7346 (mpp80) REVERT: F 282 ASN cc_start: 0.7800 (m-40) cc_final: 0.7590 (m-40) REVERT: F 308 GLU cc_start: 0.7152 (pm20) cc_final: 0.6883 (pm20) REVERT: G 33 VAL cc_start: 0.8530 (p) cc_final: 0.8193 (t) REVERT: G 37 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6617 (mt-10) REVERT: G 70 THR cc_start: 0.8102 (p) cc_final: 0.7873 (p) REVERT: G 137 GLU cc_start: 0.6855 (mp0) cc_final: 0.6472 (mp0) REVERT: G 208 ILE cc_start: 0.8578 (pt) cc_final: 0.8370 (pt) REVERT: G 296 MET cc_start: 0.7325 (mpp) cc_final: 0.7003 (mpp) REVERT: G 299 MET cc_start: 0.8037 (tpp) cc_final: 0.7703 (mmt) REVERT: G 308 GLU cc_start: 0.7087 (pm20) cc_final: 0.6785 (pm20) REVERT: G 329 GLU cc_start: 0.6630 (mt-10) cc_final: 0.6291 (mt-10) REVERT: H 50 LYS cc_start: 0.8068 (tttp) cc_final: 0.7599 (tttm) REVERT: H 63 ASN cc_start: 0.7809 (t0) cc_final: 0.7538 (t0) REVERT: H 135 ARG cc_start: 0.8162 (tpp80) cc_final: 0.7837 (ttp-170) REVERT: H 159 LYS cc_start: 0.8147 (pttm) cc_final: 0.7600 (pttm) REVERT: H 308 GLU cc_start: 0.7216 (pm20) cc_final: 0.6974 (pm20) REVERT: H 329 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.6089 (mt-10) outliers start: 59 outliers final: 41 residues processed: 802 average time/residue: 1.6011 time to fit residues: 1408.7943 Evaluate side-chains 820 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 774 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain E residue 37 GLU Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 298 ASP Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 274 MET Chi-restraints excluded: chain H residue 329 GLU Chi-restraints excluded: chain H residue 338 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN C 72 ASN C 231 ASN E 231 ASN F 231 ASN G 249 ASN H 72 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 19776 Z= 0.455 Angle : 0.610 8.773 26808 Z= 0.327 Chirality : 0.049 0.173 2936 Planarity : 0.006 0.061 3464 Dihedral : 4.849 22.818 2672 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.87 % Allowed : 20.97 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.17), residues: 2424 helix: -3.83 (0.28), residues: 48 sheet: 0.17 (0.14), residues: 1360 loop : -1.18 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 130 PHE 0.010 0.002 PHE B 333 TYR 0.041 0.002 TYR G 237 ARG 0.009 0.001 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 781 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ASP cc_start: 0.6896 (m-30) cc_final: 0.6681 (m-30) REVERT: B 202 ASP cc_start: 0.7157 (m-30) cc_final: 0.6891 (m-30) REVERT: B 308 GLU cc_start: 0.7268 (pm20) cc_final: 0.6991 (pm20) REVERT: A 39 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8170 (m) REVERT: A 226 ASP cc_start: 0.7267 (t0) cc_final: 0.6839 (t0) REVERT: A 244 ARG cc_start: 0.8511 (ttp-170) cc_final: 0.7996 (mtt180) REVERT: A 340 ARG cc_start: 0.8702 (mtm-85) cc_final: 0.8468 (mpp-170) REVERT: C 72 ASN cc_start: 0.7933 (m-40) cc_final: 0.7382 (m110) REVERT: C 246 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6864 (mtt90) REVERT: C 258 LYS cc_start: 0.8747 (ptpp) cc_final: 0.8540 (ptpp) REVERT: C 308 GLU cc_start: 0.7380 (pm20) cc_final: 0.7061 (pm20) REVERT: C 322 GLU cc_start: 0.7757 (pt0) cc_final: 0.7539 (pt0) REVERT: C 330 ASP cc_start: 0.7460 (p0) cc_final: 0.7227 (p0) REVERT: D 308 GLU cc_start: 0.7269 (pm20) cc_final: 0.7016 (pm20) REVERT: D 321 LYS cc_start: 0.7979 (mtpp) cc_final: 0.7732 (mtpp) REVERT: D 329 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6487 (mt-10) REVERT: E 37 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6862 (tt0) REVERT: E 41 GLU cc_start: 0.7161 (tt0) cc_final: 0.6926 (tt0) REVERT: E 137 GLU cc_start: 0.6691 (mp0) cc_final: 0.6383 (mp0) REVERT: E 274 MET cc_start: 0.7678 (mtp) cc_final: 0.7362 (mtp) REVERT: E 296 MET cc_start: 0.7408 (mpp) cc_final: 0.6931 (mpp) REVERT: E 302 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7717 (tpp) REVERT: E 308 GLU cc_start: 0.7386 (pm20) cc_final: 0.7097 (pm20) REVERT: F 50 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7534 (tttp) REVERT: F 69 ASP cc_start: 0.6842 (m-30) cc_final: 0.6587 (m-30) REVERT: F 90 GLU cc_start: 0.6990 (pm20) cc_final: 0.6749 (pm20) REVERT: F 229 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.7993 (m) REVERT: F 246 ARG cc_start: 0.7741 (tpp80) cc_final: 0.7327 (mpp80) REVERT: F 308 GLU cc_start: 0.7280 (pm20) cc_final: 0.7027 (pm20) REVERT: F 329 GLU cc_start: 0.6643 (mt-10) cc_final: 0.6404 (mt-10) REVERT: G 37 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6653 (mt-10) REVERT: G 90 GLU cc_start: 0.6732 (pm20) cc_final: 0.6490 (pm20) REVERT: G 133 LYS cc_start: 0.8464 (tttm) cc_final: 0.8220 (tttp) REVERT: G 137 GLU cc_start: 0.6887 (mp0) cc_final: 0.6464 (mp0) REVERT: G 299 MET cc_start: 0.8028 (tpp) cc_final: 0.7709 (mmt) REVERT: G 303 ARG cc_start: 0.8439 (mtt90) cc_final: 0.8216 (mtt180) REVERT: G 308 GLU cc_start: 0.7146 (pm20) cc_final: 0.6833 (pm20) REVERT: G 329 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6451 (mt-10) REVERT: H 50 LYS cc_start: 0.8185 (tttp) cc_final: 0.7679 (tttm) REVERT: H 135 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7931 (ttp-170) REVERT: H 159 LYS cc_start: 0.8186 (pttm) cc_final: 0.7555 (pttm) REVERT: H 308 GLU cc_start: 0.7328 (pm20) cc_final: 0.7085 (pm20) REVERT: H 329 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6416 (mt-10) outliers start: 62 outliers final: 42 residues processed: 794 average time/residue: 1.6601 time to fit residues: 1442.0574 Evaluate side-chains 824 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 773 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 169 TYR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 169 TYR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 241 MET Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 GLU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 298 ASP Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 340 ARG Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 274 MET Chi-restraints excluded: chain H residue 329 GLU Chi-restraints excluded: chain H residue 338 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 169 optimal weight: 0.0870 chunk 66 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 203 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 231 ASN D 316 ASN E 231 ASN F 231 ASN G 249 ASN H 63 ASN H 72 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19776 Z= 0.251 Angle : 0.559 8.085 26808 Z= 0.303 Chirality : 0.048 0.159 2936 Planarity : 0.006 0.060 3464 Dihedral : 4.607 20.022 2672 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.36 % Allowed : 21.94 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.17), residues: 2424 helix: -2.33 (0.42), residues: 96 sheet: 0.07 (0.14), residues: 1400 loop : -1.52 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 217 PHE 0.008 0.001 PHE F 100 TYR 0.031 0.001 TYR H 237 ARG 0.008 0.001 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 784 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ASP cc_start: 0.6849 (m-30) cc_final: 0.6628 (m-30) REVERT: B 202 ASP cc_start: 0.7162 (m-30) cc_final: 0.6900 (m-30) REVERT: B 308 GLU cc_start: 0.7208 (pm20) cc_final: 0.6934 (pm20) REVERT: A 226 ASP cc_start: 0.7210 (t0) cc_final: 0.6762 (t0) REVERT: A 244 ARG cc_start: 0.8434 (ttp-170) cc_final: 0.7881 (mtt180) REVERT: C 246 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6673 (mtt90) REVERT: C 308 GLU cc_start: 0.7288 (pm20) cc_final: 0.6969 (pm20) REVERT: C 322 GLU cc_start: 0.7742 (pt0) cc_final: 0.7531 (pt0) REVERT: C 330 ASP cc_start: 0.7398 (p0) cc_final: 0.7182 (p0) REVERT: D 72 ASN cc_start: 0.8280 (m110) cc_final: 0.8001 (m110) REVERT: D 132 LYS cc_start: 0.8157 (ttpt) cc_final: 0.7855 (ttpt) REVERT: D 308 GLU cc_start: 0.7171 (pm20) cc_final: 0.6906 (pm20) REVERT: D 321 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7675 (mtpp) REVERT: D 329 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6419 (mt-10) REVERT: E 37 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6853 (tt0) REVERT: E 41 GLU cc_start: 0.7126 (tt0) cc_final: 0.6904 (tt0) REVERT: E 137 GLU cc_start: 0.6658 (mp0) cc_final: 0.6377 (mp0) REVERT: E 274 MET cc_start: 0.7558 (mtp) cc_final: 0.7254 (mtp) REVERT: E 302 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7677 (tpp) REVERT: E 308 GLU cc_start: 0.7310 (pm20) cc_final: 0.7049 (pm20) REVERT: F 69 ASP cc_start: 0.6804 (m-30) cc_final: 0.6538 (m-30) REVERT: F 90 GLU cc_start: 0.6977 (pm20) cc_final: 0.6748 (pm20) REVERT: F 167 ILE cc_start: 0.8149 (mp) cc_final: 0.7824 (mp) REVERT: F 246 ARG cc_start: 0.7595 (tpp80) cc_final: 0.7217 (mpp80) REVERT: F 308 GLU cc_start: 0.7180 (pm20) cc_final: 0.6929 (pm20) REVERT: F 329 GLU cc_start: 0.6561 (mt-10) cc_final: 0.6346 (mt-10) REVERT: G 33 VAL cc_start: 0.8576 (p) cc_final: 0.8242 (t) REVERT: G 37 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6682 (mt-10) REVERT: G 70 THR cc_start: 0.8113 (p) cc_final: 0.7886 (p) REVERT: G 90 GLU cc_start: 0.6778 (pm20) cc_final: 0.6479 (pm20) REVERT: G 137 GLU cc_start: 0.6865 (mp0) cc_final: 0.6476 (mp0) REVERT: G 301 ILE cc_start: 0.8646 (mp) cc_final: 0.8383 (mt) REVERT: G 308 GLU cc_start: 0.7025 (pm20) cc_final: 0.6739 (pm20) REVERT: G 329 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6330 (mt-10) REVERT: H 50 LYS cc_start: 0.8085 (tttp) cc_final: 0.7731 (tttm) REVERT: H 72 ASN cc_start: 0.7954 (OUTLIER) cc_final: 0.7738 (m110) REVERT: H 135 ARG cc_start: 0.8187 (tpp80) cc_final: 0.7829 (ttp-170) REVERT: H 159 LYS cc_start: 0.8149 (pttm) cc_final: 0.7638 (pttm) REVERT: H 308 GLU cc_start: 0.7241 (pm20) cc_final: 0.6996 (pm20) REVERT: H 329 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6320 (mt-10) outliers start: 51 outliers final: 36 residues processed: 791 average time/residue: 1.6873 time to fit residues: 1460.3323 Evaluate side-chains 803 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 761 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 241 MET Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 GLU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 298 ASP Chi-restraints excluded: chain G residue 128 MET Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 72 ASN Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 329 GLU Chi-restraints excluded: chain H residue 338 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 190 optimal weight: 0.2980 chunk 19 optimal weight: 0.5980 chunk 147 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 ASN C 231 ASN E 231 ASN F 231 ASN G 249 ASN H 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19776 Z= 0.252 Angle : 0.570 7.916 26808 Z= 0.309 Chirality : 0.048 0.162 2936 Planarity : 0.006 0.070 3464 Dihedral : 4.611 18.647 2672 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.81 % Allowed : 23.19 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.17), residues: 2424 helix: -2.27 (0.42), residues: 96 sheet: 0.07 (0.14), residues: 1400 loop : -1.54 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 217 PHE 0.009 0.001 PHE H 100 TYR 0.044 0.001 TYR H 237 ARG 0.007 0.001 ARG G 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 777 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 ASP cc_start: 0.6848 (m-30) cc_final: 0.6613 (m-30) REVERT: B 132 LYS cc_start: 0.8383 (ttpp) cc_final: 0.8072 (ttpt) REVERT: B 202 ASP cc_start: 0.7170 (m-30) cc_final: 0.6903 (m-30) REVERT: B 308 GLU cc_start: 0.7234 (pm20) cc_final: 0.6972 (pm20) REVERT: A 218 ASP cc_start: 0.7226 (m-30) cc_final: 0.7026 (m-30) REVERT: A 226 ASP cc_start: 0.7190 (t0) cc_final: 0.6761 (t0) REVERT: C 33 VAL cc_start: 0.8506 (p) cc_final: 0.8164 (t) REVERT: C 72 ASN cc_start: 0.7931 (m-40) cc_final: 0.7454 (m110) REVERT: C 231 ASN cc_start: 0.8169 (m110) cc_final: 0.7958 (m-40) REVERT: C 246 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6643 (mtt90) REVERT: C 308 GLU cc_start: 0.7334 (pm20) cc_final: 0.7017 (pm20) REVERT: C 322 GLU cc_start: 0.7740 (pt0) cc_final: 0.7510 (pt0) REVERT: C 330 ASP cc_start: 0.7405 (p0) cc_final: 0.7199 (p0) REVERT: D 72 ASN cc_start: 0.8274 (m110) cc_final: 0.7991 (m110) REVERT: D 132 LYS cc_start: 0.8171 (ttpt) cc_final: 0.7848 (ttpt) REVERT: D 308 GLU cc_start: 0.7163 (pm20) cc_final: 0.6891 (pm20) REVERT: D 321 LYS cc_start: 0.7900 (mtpp) cc_final: 0.7675 (mtpp) REVERT: D 329 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6439 (mt-10) REVERT: E 37 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6710 (tt0) REVERT: E 41 GLU cc_start: 0.7127 (tt0) cc_final: 0.6912 (tt0) REVERT: E 137 GLU cc_start: 0.6670 (mp0) cc_final: 0.6386 (mp0) REVERT: E 296 MET cc_start: 0.7420 (mpp) cc_final: 0.6837 (mpp) REVERT: E 302 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7735 (tpp) REVERT: E 308 GLU cc_start: 0.7311 (pm20) cc_final: 0.7054 (pm20) REVERT: E 330 ASP cc_start: 0.7315 (p0) cc_final: 0.7097 (p0) REVERT: F 50 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7341 (tttp) REVERT: F 69 ASP cc_start: 0.6797 (m-30) cc_final: 0.6529 (m-30) REVERT: F 90 GLU cc_start: 0.6937 (pm20) cc_final: 0.6696 (pm20) REVERT: F 91 MET cc_start: 0.8196 (mtm) cc_final: 0.7978 (mtp) REVERT: F 246 ARG cc_start: 0.7452 (tpp80) cc_final: 0.7203 (tpp80) REVERT: F 282 ASN cc_start: 0.7805 (m-40) cc_final: 0.7597 (m-40) REVERT: F 308 GLU cc_start: 0.7183 (pm20) cc_final: 0.6931 (pm20) REVERT: F 329 GLU cc_start: 0.6556 (mt-10) cc_final: 0.6342 (mt-10) REVERT: G 33 VAL cc_start: 0.8575 (p) cc_final: 0.8234 (t) REVERT: G 37 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6685 (mt-10) REVERT: G 70 THR cc_start: 0.8102 (p) cc_final: 0.7876 (p) REVERT: G 90 GLU cc_start: 0.6737 (pm20) cc_final: 0.6434 (pm20) REVERT: G 106 ARG cc_start: 0.8030 (mtp85) cc_final: 0.7815 (mtp180) REVERT: G 137 GLU cc_start: 0.6860 (mp0) cc_final: 0.6472 (mp0) REVERT: G 301 ILE cc_start: 0.8658 (mp) cc_final: 0.8395 (mt) REVERT: G 308 GLU cc_start: 0.7048 (pm20) cc_final: 0.6765 (pm20) REVERT: G 329 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6330 (mt-10) REVERT: H 50 LYS cc_start: 0.8099 (tttp) cc_final: 0.7754 (tttm) REVERT: H 63 ASN cc_start: 0.7826 (t0) cc_final: 0.7535 (t0) REVERT: H 135 ARG cc_start: 0.8167 (tpp80) cc_final: 0.7804 (ttp-170) REVERT: H 159 LYS cc_start: 0.8154 (pttm) cc_final: 0.7642 (pttm) REVERT: H 208 ILE cc_start: 0.8513 (pt) cc_final: 0.8283 (pt) REVERT: H 308 GLU cc_start: 0.7245 (pm20) cc_final: 0.6999 (pm20) REVERT: H 329 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6226 (mt-10) outliers start: 39 outliers final: 31 residues processed: 785 average time/residue: 1.7106 time to fit residues: 1470.7589 Evaluate side-chains 808 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 771 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 241 MET Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 GLU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 329 GLU Chi-restraints excluded: chain H residue 338 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.4980 chunk 202 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 175 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 52 optimal weight: 5.9990 chunk 190 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 ASN ** F 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 ASN ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.116956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.108181 restraints weight = 27758.903| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.89 r_work: 0.3333 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19776 Z= 0.241 Angle : 0.570 8.215 26808 Z= 0.308 Chirality : 0.048 0.160 2936 Planarity : 0.005 0.062 3464 Dihedral : 4.576 19.749 2672 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.85 % Allowed : 23.66 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.17), residues: 2424 helix: -2.27 (0.42), residues: 96 sheet: 0.08 (0.14), residues: 1400 loop : -1.53 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 217 PHE 0.010 0.001 PHE H 100 TYR 0.034 0.001 TYR H 237 ARG 0.008 0.001 ARG D 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16666.83 seconds wall clock time: 291 minutes 52.84 seconds (17512.84 seconds total)